Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling

doi:10.1038/s41591-020-1000-7

. 2020 Sep;26(9):1398-1404.

doi: 10.1038/s41591-020-1000-7. Epub 2020 Jul 9.

Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling

Rebecca J Rockett^#^{1

2}, Alicia Arnott^#^{1

2

3}, Connie Lam^{1

2}, Rosemarie Sadsad^{1

2

4}, Verlaine Timms^{1

2}, Karen-Ann Gray^{1

2}, John-Sebastian Eden^{1

5}, Sheryl Chang⁶, Mailie Gall³, Jenny Draper³, Eby M Sim^{2

3}, Nathan L Bachmann^{2

3}, Ian Carter³, Kerri Basile³, Roy Byun⁷, Matthew V O'Sullivan^{1

2

3}, Sharon C-A Chen^{1

2

3}, Susan Maddocks³, Tania C Sorrell^{1

2

8}, Dominic E Dwyer^{1

2

3}, Edward C Holmes^{1

9}, Jen Kok^{1

2

3}, Mikhail Prokopenko^{1

6}, Vitali Sintchenko^{10

11

12

13}

Affiliations

¹ Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia.
² Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia.
³ Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead, New South Wales, Australia.
⁴ Sydney Informatics Hub, Core Research Facilities, University of Sydney, Sydney, New South Wales, Australia.
⁵ Centre for Virus Research, Westmead Institute for Medical Research, Westmead, New South Wales, Australia.
⁶ Centre for Complex Systems, Faculty of Engineering, University of Sydney, Sydney, New South Wales, Australia.
⁷ Health Protection NSW, NSW Ministry of Health, Sydney, New South Wales, Australia.
⁸ Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia.
⁹ School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia.
¹⁰ Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia. vitali.sintchenko@sydney.edu.au.
¹¹ Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia. vitali.sintchenko@sydney.edu.au.
¹² Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead, New South Wales, Australia. vitali.sintchenko@sydney.edu.au.
¹³ Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia. vitali.sintchenko@sydney.edu.au.

^# Contributed equally.

PMID: 32647358
DOI: 10.1038/s41591-020-1000-7

Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling

Rebecca J Rockett et al. Nat Med. 2020 Sep.

. 2020 Sep;26(9):1398-1404.

doi: 10.1038/s41591-020-1000-7. Epub 2020 Jul 9.

Authors

Affiliations

¹ Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia.
² Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia.
³ Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead, New South Wales, Australia.
⁴ Sydney Informatics Hub, Core Research Facilities, University of Sydney, Sydney, New South Wales, Australia.
⁵ Centre for Virus Research, Westmead Institute for Medical Research, Westmead, New South Wales, Australia.
⁶ Centre for Complex Systems, Faculty of Engineering, University of Sydney, Sydney, New South Wales, Australia.
⁷ Health Protection NSW, NSW Ministry of Health, Sydney, New South Wales, Australia.
⁸ Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia.
⁹ School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia.
¹⁰ Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia. vitali.sintchenko@sydney.edu.au.
¹¹ Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia. vitali.sintchenko@sydney.edu.au.
¹² Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead, New South Wales, Australia. vitali.sintchenko@sydney.edu.au.
¹³ Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia. vitali.sintchenko@sydney.edu.au.

^# Contributed equally.

PMID: 32647358
DOI: 10.1038/s41591-020-1000-7

Abstract

In January 2020, a novel betacoronavirus (family Coronaviridae), named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified as the etiological agent of a cluster of pneumonia cases occurring in Wuhan City, Hubei Province, China^1,2. The disease arising from SARS-CoV-2 infection, coronavirus disease 2019 (COVID-19), subsequently spread rapidly causing a worldwide pandemic. Here we examine the added value of near real-time genome sequencing of SARS-CoV-2 in a subpopulation of infected patients during the first 10 weeks of COVID-19 containment in Australia and compare findings from genomic surveillance with predictions of a computational agent-based model (ABM). Using the Australian census data, the ABM generates over 24 million software agents representing the population of Australia, each with demographic attributes of an anonymous individual. It then simulates transmission of the disease over time, spreading from specific infection sources, using contact rates of individuals within different social contexts. We report that the prospective sequencing of SARS-CoV-2 clarified the probable source of infection in cases where epidemiological links could not be determined, significantly decreased the proportion of COVID-19 cases with contentious links, documented genomically similar cases associated with concurrent transmission in several institutions and identified previously unsuspected links. Only a quarter of sequenced cases appeared to be locally acquired and were concordant with predictions from the ABM. These high-resolution genomic data are crucial to track cases with locally acquired COVID-19 and for timely recognition of independent importations once border restrictions are lifted and trade and travel resume.

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References

1. Wu, F. et al. A new coronavirus associated with human respiratory disease in China. Nature 579, 265–269 (2020). - PubMed - PMC - DOI
1. Coronavirus Disease 2019 (COVID-19). Situation Report 48 https://www.who.int/docs/default-source/coronaviruse/situation-reports/2... (World Health Organization, 2020).
1. Coronavirus Disease 2019 (COVID-19). Situation Report 67 https://www.who.int/docs/default-source/coronaviruse/situation-reports/2... (World Health Organization, 2020).
1. Li, R. et al. Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV2). Science 368, 489–493 (2020). - PubMed - PMC - DOI
1. Ghinai, I. et al. First known person-to-person transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the USA. Lancet 395, 1137–1144 (2020). - PubMed - PMC - DOI

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[1] Wu, F. et al. A new coronavirus associated with human respiratory disease in China. Nature 579, 265–269 (2020). - PubMed - PMC - DOI

[2] Wu, F. et al. A new coronavirus associated with human respiratory disease in China. Nature 579, 265–269 (2020). - PubMed - PMC - DOI

[3] Coronavirus Disease 2019 (COVID-19). Situation Report 48 https://www.who.int/docs/default-source/coronaviruse/situation-reports/2... (World Health Organization, 2020).

[4] Coronavirus Disease 2019 (COVID-19). Situation Report 48 https://www.who.int/docs/default-source/coronaviruse/situation-reports/2... (World Health Organization, 2020).

[5] Coronavirus Disease 2019 (COVID-19). Situation Report 67 https://www.who.int/docs/default-source/coronaviruse/situation-reports/2... (World Health Organization, 2020).

[6] Coronavirus Disease 2019 (COVID-19). Situation Report 67 https://www.who.int/docs/default-source/coronaviruse/situation-reports/2... (World Health Organization, 2020).

[7] Li, R. et al. Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV2). Science 368, 489–493 (2020). - PubMed - PMC - DOI

[8] Li, R. et al. Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV2). Science 368, 489–493 (2020). - PubMed - PMC - DOI

[9] Ghinai, I. et al. First known person-to-person transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the USA. Lancet 395, 1137–1144 (2020). - PubMed - PMC - DOI

[10] Ghinai, I. et al. First known person-to-person transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the USA. Lancet 395, 1137–1144 (2020). - PubMed - PMC - DOI

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Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling

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Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling

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